/**
 * PHOSIDE: PHosphorylation Site IDentification Engine.
 * Copyright 2009 Digital Biology Lab, University of Missouri.
 * This library is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 3 of the License, or (at your option) any later
 * version. <p/> This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the License for more
 * details.
 */

package phoside.io.fasta;

import phoside.io.fasta.parser.DefaultPhosphoSequenceParser;

import java.util.Set;

import phoside.PhosphoProteins;

import phoside.io.fasta.parser.HeaderRule;
import phoside.io.fasta.parser.DefaultHeaderParser;

public class PhosphoReaderFastaVisitorWithSitesInSequence extends ProteinsReaderFastaVisitor {
//    public PhosphoReaderFastaVisitorWithSitesInSequence(final PhosphoProteins phosphoData,
//            final HeaderRule rule) {
//        this(phosphoData, rule, new DefaultPhosphoSequenceParser("#"));
//    }

    public PhosphoReaderFastaVisitorWithSitesInSequence(final PhosphoProteins phosphoData,
            final HeaderRule rule, DefaultPhosphoSequenceParser sequenceParser) {
        super(phosphoData, new DefaultHeaderParser(rule), sequenceParser);
    }

    /**
     *
     * @param header
     * @param sequence
     */
    @Override
    public void visit(final String header, final String sequence) {
        super.visit(header, sequence);
        
        String accession = headerParser.getAccession();
        if (accession != null) {
            Set<Integer> sites = ((DefaultPhosphoSequenceParser)sequenceParser).getSites();
            if (sites!=null) {
                ((PhosphoProteins)proteins).addSites(accession, sites);
            }
        }
    }

}
